Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography.
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Han G, Ye M, Zhou H, Jiang X, Feng S, Jiang X, Tian R, Wan D, Zou H, Gu J
Large-scale phosphoproteome analysis of human liver tissue by enrichment and fractionation of phosphopeptides with strong anion exchange chromatography.
Proteomics. 2008 Apr;8(7):1346-61. doi: 10.1002/pmic.200700884.
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18318008 [View in PubMed]
- Abstract
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The mixture of phosphopeptides enriched from proteome samples are very complex. To reduce the complexity it is necessary to fractionate the phosphopeptides. However, conventional enrichment methods typically only enrich phosphopeptides but not fractionate phosphopeptides. In this study, the application of strong anion exchange (SAX) chromatography for enrichment and fractionation of phosphopeptides was presented. It was found that phosphopeptides were highly enriched by SAX and majority of unmodified peptides did not bind onto SAX. Compared with Fe(3+) immobilized metal affinity chromatography (Fe(3+)-IMAC), almost double phosphopeptides were identified from the same sample when only one fraction was generated by SAX. SAX and Fe(3+)-IMAC showed the complementarity in enrichment and identification of phosphopeptides. It was also demonstrated that SAX have the ability to fractionate phosphopeptides under gradient elution based on their different interaction with SAX adsorbent. SAX was further applied to enrich and fractionate phosphopeptides in tryptic digest of proteins extracted from human liver tissue adjacent to tumorous region for phosphoproteome profiling. This resulted in the highly confident identification of 274 phosphorylation sites from 305 unique phosphopeptides corresponding to 168 proteins at false discovery rate (FDR) of 0.96%.
DrugBank Data that Cites this Article
- Polypeptides
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Name UniProt ID Ferritin heavy chain P02794 Details Serum albumin P02768 Details Ryanodine receptor 1 P21817 Details 5'-AMP-activated protein kinase subunit beta-2 O43741 Details Thiopurine S-methyltransferase P51580 Details Calnexin P27824 Details Heat shock protein HSP 90-alpha P07900 Details Fibronectin P02751 Details Heat shock protein HSP 90-beta P08238 Details Histone deacetylase 1 Q13547 Details Prostaglandin E synthase 3 Q15185 Details cAMP-dependent protein kinase type II-alpha regulatory subunit P13861 Details cAMP-dependent protein kinase type I-alpha regulatory subunit P10644 Details Cation-independent mannose-6-phosphate receptor P11717 Details Proteasome subunit alpha type-3 P25788 Details Calcium/calmodulin-dependent protein kinase type II subunit delta Q13557 Details Myosin-11 P35749 Details cAMP-dependent protein kinase type II-beta regulatory subunit P31323 Details 14-3-3 protein epsilon P62258 Details Membrane-associated progesterone receptor component 1 O00264 Details Nucleolar and coiled-body phosphoprotein 1 Q14978 Details Hepatoma-derived growth factor P51858 Details Protein S100-A9 P06702 Details Alpha-2-HS-glycoprotein P02765 Details Heterogeneous nuclear ribonucleoprotein D0 Q14103 Details Nucleophosmin P06748 Details Myosin-9 P35579 Details Myosin light chain kinase, smooth muscle Q15746 Details Serine/threonine-protein kinase OSR1 O95747 Details